Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana
Mary M Rorick, Edward B Baskerville, Thomas S Rask, Karen P Day, Mercedes Pascual
PLOS COMPUTATIONAL BIOLOGY | PUBLIC LIBRARY SCIENCE | Published : 2018
A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation. Functional changes can in some cases be tracked through the evolutionary history of a gene family; however phylogenetic approaches are not possible in cases where gene families diversify primarily by recombination. We take a network theoretical approach to functionally classify the highly recombining var antigenic gene family of the malaria parasite Plasmodium falciparum. We sample var DBLα sequence types from a local population in Ghana, and classify 9,276 of these variants into just 48 functional types. Our approach is to first decompose each sequence type in..View full abstract
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Awarded by Fogarty International Center at National Institutes of Health Program on the Ecology and Evolution of Infectious Diseases (EEID)
Awarded by National Institute of Allergy and Infectious Disease, National Institutes of Health
This work was funded by: Fogarty International Center at National Institutes of Health Program on the Ecology and Evolution of Infectious Diseases (EEID) [Grant number: R01-TW009670]; and the National Institute of Allergy and Infectious Disease, National Institutes of Health [Grant number: R01-A1084156]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.